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Andre Asena, Shaun Thomas Smith, Tanya Kairn, Scott Bradley Crowe, Kazuyuki Hosokawa, Steven Sylvander, Jamie Vincent Trapp
PURPOSE: In this work, we develop a methodology for using Fricke gel dosimeters for dose distribution measurements surrounding high-density implants which circumvents artefact production by removing the obstruction during imaging. METHODS: Custom 3D printed moulds were used to set cavities in Fricke gel phantoms to allow for the suspension of high density implants in different geometries. This allowed for the metal valve extracted from a temporary tissue expander to be suspended during irradiation, and removed during optical-CT scanning...
January 17, 2017: Medical Physics
Katarzyna Zaremba-Niedzwiedzka, Eva F Caceres, Jimmy H Saw, Disa Bäckström, Lina Juzokaite, Emmelien Vancaester, Kiley W Seitz, Karthik Anantharaman, Piotr Starnawski, Kasper U Kjeldsen, Matthew B Stott, Takuro Nunoura, Jillian F Banfield, Andreas Schramm, Brett J Baker, Anja Spang, Thijs J G Ettema
The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota...
January 11, 2017: Nature
Oliver Trapp, Mascha Fiedler, Michael Hartwich, Martin Schorl, Armin Kalenka
BACKGROUND: The weaning target in tracheotomised patients is not extubation, but spontaneous breathing without the support of a ventilator. Overloading the respiratory pump during such spontaneous breathing trials is unfavorable, prolongs weaning time, and increases morbidity and mortality. The goal of this study was to evaluate the electrical activity of the diaphragm during a t-piece trial in non-communicative neurological patients and the comparison to clinical parameters of exhaustion...
January 6, 2017: Neurocritical Care
Martin Bach, Mirjam Diesner, Dietlinde Großmann, Djamal Guerniche, Udo Hommen, Michael Klein, Roland Kubiak, Alexandra Müller, Thomas G Preuss, Jan Priegnitz, Stefan Reichenberger, Kai Thomas, Matthias Trapp
BACKGROUND: In order to assess surface water exposure to active substances of plant protection products (PPP) in the EU, the FOCUS (FOrum for the Co-ordination of pesticide fate models and their USe) surface water workgroup introduced four runoff and six drainage scenarios for Step 3 of the tiered FOCUSsw approach. These scenarios may not necessarily represent realistic worst-case situations for the different Member States of the EU. Hence, the suitability of the scenarios for risk assessment in the national authorisation procedures is not known...
January 6, 2017: Pest Management Science
Gwenaelle Begue, Ulrika Raue, Bozena Jemiolo, Scott W Trappe
A new application of the Reduced Representation Bisulfite Sequencing method was developed using low-DNA input to investigate the epigenetic profile of human slow- and fast-twitch skeletal muscle fibers. Successful library construction was completed with as little as 15 ng of DNA and high quality sequencing data were obtained with 32 ng of DNA. Analysis identified 143,160 differentially methylated CpG-sites across 14,046 genes. In both fiber types, selected genes predominantly expressed in slow or fast fibers were hypomethylated, which was supported by the RNA-Seq analysis...
January 5, 2017: Journal of Applied Physiology
Stephan Kiontke, Lars Langemeyer, Anne Kuhlee, Saskia Schuback, Stefan Raunser, Christian Ungermann, Daniel Kümmel
The Mon1-Ccz1 complex (MC1) is the guanine nucleotide exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 and is required for endosomal maturation and fusion at the vacuole/lysosome. Here we present the overall architecture of MC1 from Chaetomium thermophilum, and in combining biochemical studies and mutational analysis in yeast, we identify the domains required for catalytic activity, complex assembly and localization of MC1. The crystal structure of a catalytic MC1 core complex bound to Ypt7 provides mechanistic insight into its function...
January 4, 2017: Nature Communications
Miguel Jorge, Nuno M Garrido, Carlos J V Simões, Cândida G Silva, Rui M M Brito
We present a systematic test of the performance of three popular united-atom force fields-OPLS-UA, GROMOS and TraPPE-at predicting hydrophobic solvation, more precisely at describing the solvation of alkanes in alkanes. Gibbs free energies of solvation were calculated for 52 solute/solvent pairs from Molecular Dynamics simulations and thermodynamic integration making use of the IBERCIVIS volunteer computing platform. Our results show that all force fields yield good predictions when both solute and solvent are small linear or branched alkanes (up to pentane)...
March 5, 2017: Journal of Computational Chemistry
Judith Trapp, Alison McAfee, Leonard J Foster
Globally, there are over 20,000 bee species (Hymenoptera: Apoidea: Anthophila) with a host of biologically fascinating characteristics. Though they have long been studied as models for social evolution, recent challenges to bee health (mainly diseases and pesticides) have gathered the attention of both the public and the research community. Genome sequences of twelve bee species are now complete or under progress, facilitating the application of additional 'omic technologies. Here we review recent developments in honey bee and native bee research in the genomic era...
December 27, 2016: Molecular Ecology
Chunman Li, Xiaomin Luo, Shan Zhao, Gavin Ky Siu, Yongheng Liang, Hsiao Chang Chan, Ayano Satoh, Sidney Sb Yu
The transport protein particle (TRAPP) was initially identified as a vesicle tethering factor in yeast and as a guanine nucleotide exchange factor (GEF) for Ypt1/Rab1. In mammals, structures and functions of various TRAPP complexes are beginning to be understood. We found that mammalian TRAPPII was a GEF for both Rab18 and Rab1. Inactivation of TRAPPII-specific subunits by various methods including siRNA depletion and CRISPR-Cas9-mediated deletion reduced lipolysis and resulted in aberrantly large lipid droplets...
December 21, 2016: EMBO Journal
Oliver Dumele, Benedikt Schreib, Ulrike Warzok, Nils Trapp, Christoph A Schalley, François Diederich
Supramolecular capsules were assembled by neutral halogen bonding (XB) and studied in the solid state, in solution, and in the gas phase. The geometry of the highly organized capsules is shown by an X-ray crystal structure which features the assembly of two XB hemispheres, geometrically rigidified by H-bonding to eight MeOH molecules and encapsulation of two benzene guests. To enhance capsular association strength, tuning the XB donor is more efficient than tuning the XB acceptor, due to desolvation penalties in protic solvents, as shown for a tetraquinuclidine XB acceptor hemisphere...
December 21, 2016: Angewandte Chemie
Ralf U Trappe, Daan Dierickx, Heiner Zimmermann, Franck Morschhauser, Peter Mollee, Jan M Zaucha, Martin H Dreyling, Ulrich Dührsen, Petra Reinke, Gregor Verhoef, Marion Subklewe, Andreas Hüttmann, Thomas Tousseyn, Gilles Salles, Volker Kliem, Ingeborg A Hauser, Corrado Tarella, Eric Van Den Neste, Olivier Gheysens, Ioannis Anagnostopoulos, Veronique Leblond, Hanno Riess, Sylvain Choquet
Purpose The Sequential Treatment of CD20-Positive Posttransplant Lymphoproliferative Disorder (PTLD-1) trial ( identifier, NCT01458548) established sequential treatment with four cycles of rituximab followed by four cycles of cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) chemotherapy as a standard in the management of post-transplant lymphoproliferative disorder (PTLD) and identified response to rituximab induction as a prognostic factor for overall survival. We hypothesized that rituximab consolidation might be sufficient treatment for patients with a complete response after rituximab induction...
December 19, 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
Maude Giroud, Jakov Ivkovic, Mara Martignoni, Marianne Fleuti, Nils Trapp, Wolfgang Haap, Andreas Kuglstatter, Jörg Benz, Bernd Kuhn, Tanja Schirmeister, Francois Diederich
We report an extensive "heteroarene scan" of triazine nitrile ligands of the cysteine protease human cathepsin L (hCatL) to investigate -stacking on the peptide amide bond Gly67-Gly68 at the entrance of the S3 pocket. This heteroarene···peptide bond stacking was supported by a co-crystal structure of an imidazopyridine ligand with hCatL. Inhibitory constants Ki are strongly influenced by the diverse nature of the heterocycles and specific interactions with the local environment of the S3 pocket. Binding affinities vary by three orders of magnitude...
December 19, 2016: ChemMedChem
Madhu Kamle, Einat Bar, Dalia Lewinsohn, Elinoar Shavit, Nurit Roth-Bejerano, Varda Kagan-Zur, Ofer Guy, Eli Zaadi, Efraim Lewinsohn, Yaron Sitrit
Desert truffles are mycorrhizal, hypogeous fungi considered a delicacy. Based on morphological characters, we identified three desert truffles species that grow in the same habitat in the Negev desert. These include Picoa lefebvrei (Pat.), Tirmania nivea (Desf.) Trappe, and Terfezia boudieri (Chatain), all associated with Helianthemum sessiliflorum. Their taxonomy was confirmed by PCR-RFLP. The main volatiles of fruit bodies of T. boudieri and T. nivea were 1-octen-3-ol and hexanal, however volatiles of the latter species further included branched chain amino acid derivatives such as 2-methylbutanal and 3-methylbutanal, phenylalanine derivatives such as benzaldehyde and benzenacetaldehyde, and methionine derivatives such as methional and dimethyldisulfide...
December 17, 2016: Journal of Agricultural and Food Chemistry
Klaus Müller, Raffael Vorberg, Nils Trapp, Erick M Carreira
The synthesis and X-ray crystal structures of syn and anti 4-N-Boc-aminobicyclo[3.2.0]heptan-1-carboxylic acids are described. The placement of the N-Boc-amino groups in the two stereoisomers in either pseudo-equatorial or pseudo-axial positions render the molecules conformationally locked N-Boc-protected alpha-aminobutyric acid (GABA) embedded within the bicyclic core. Despite the different conformations of the urethane and distinct crystal packing, the bicyclic core units of the two stereoisomers adopt virtually identical structures...
December 15, 2016: Chemistry: a European Journal
Othonas A Moultos, Ioannis N Tsimpanogiannis, Athanassios Z Panagiotopoulos, J P Martin Trusler, Ioannis G Economou
Atomistic molecular dynamics simulations were carried out to obtain the diffusion coefficients of CO2 in n-hexane, n-decane, n-hexadecane, cyclohexane, and squalane at temperatures up to 423.15 K and pressures up to 65 MPa. Three popular models were used for the representation of hydrocarbons: the united atom TraPPE (TraPPE-UA), the all-atom OPLS, and an optimized version of OPLS, namely, L-OPLS. All models qualitatively reproduce the pressure dependence of the diffusion coefficient of CO2 in hydrocarbons measured recently, and L-OPLS was found to be the most accurate...
December 22, 2016: Journal of Physical Chemistry. B
Hayley Christian, Clover Maitland, Stephanie Enkel, Georgina Trapp, Stewart G Trost, Jasper Schipperijn, Bryan Boruff, Leanne Lester, Michael Rosenberg, Stephen R Zubrick
INTRODUCTION: The early years are a critical period in a child's health and development, yet most preschool children fail to meet physical activity guidelines. Outside of the home and neighbourhood, children spend a large proportion of time within early childhood education and care (ECEC) services such as long day care. Research is required to determine how the design of day care outdoor (and indoor) spaces provides opportunities or constraints for physical activity. A significant evidence gap surrounds what objectively measured attributes of the home and neighbourhood environment influence preschoolers' physical activity...
December 8, 2016: BMJ Open
Sujan Mamidi, Phillip N Miklas, Jennifer Trapp, Erin Felicetti, Jane Grimwood, Jeremy Schmutz, Rian Lee, Phillip E McClean
White mold, caused by the necrotrophic fungus (Lib.) de Bary, is a major disease of common bean ( L.). WM7.1 and WM8.3 are two quantitative trait loci (QTL) with major effects on tolerance to the pathogen. Advanced backcross populations segregating individually for either of the two QTL, and a recombinant inbred (RI) population segregating for both QTL were used to fine map and confirm the genetic location of the QTL. The QTL intervals were physically mapped using the reference common bean genome sequence, and the physical intervals for each QTL were further confirmed by sequence-based introgression mapping...
July 2016: Plant Genome
Greg J Grosicki, Robert A Standley, Kevin A Murach, Ulrika Raue, Kiril Minchev, Paul M Coen, Stephen Kritchevsky, Bret H Goodpaster, Scott Trappe
No abstract text is available yet for this article.
November 1, 2016: Journal of Applied Physiology
Xinghua Yin, Grahame J Kidd, Nobuhiko Ohno, Guy A Perkins, Mark H Ellisman, Chinthasagar Bastian, Sylvain Brunet, Selva Baltan, Bruce D Trapp
Hereditary spastic paraplegia (HSP) is a neurological syndrome characterized by degeneration of central nervous system (CNS) axons. Mutated HSP proteins include myelin proteolipid protein (PLP) and axon-enriched proteins involved in mitochondrial function, smooth endoplasmic reticulum (SER) structure, and microtubule (MT) stability/function. We characterized axonal mitochondria, SER, and MTs in rodent optic nerves where PLP is replaced by the peripheral nerve myelin protein, P0 (P0-CNS mice). Mitochondrial pathology and degeneration were prominent in juxtaparanodal axoplasm at 1 mo of age...
November 21, 2016: Journal of Cell Biology
Laura L Thomas, J Christopher Fromme
Rab guanosine triphosphatases (GTPases) control cellular trafficking pathways by regulating vesicle formation, transport, and tethering. Rab11 and its paralogs regulate multiple secretory and endocytic recycling pathways, yet the guanine nucleotide exchange factor (GEF) that activates Rab11 in most eukaryotic cells is unresolved. The large multisubunit transport protein particle (TRAPP) II complex has been proposed to act as a GEF for Rab11 based on genetic evidence, but conflicting biochemical experiments have created uncertainty regarding Rab11 activation...
November 21, 2016: Journal of Cell Biology
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